5DPW	Protein Binding	date	Sep 14, 2015
title	Crystal Structure Of Plekhm1 Lir In Complex With Human Lc3c_
authors	A.C.Ravichandran, H.Suzuki, R.C.J.Dobson
compound		source
Molecule: Microtubule-Associated Proteins 1a1b Light Chain Chain: A, C, E, G, I, K, M, O Fragment: Unp Residues 8-125 Synonym: Autophagy-Related Protein Lc3 C,Autophagy-Related Like Modifier Lc3 C,Map1 Light Chain 3-Like Protein 3,Map1a Light Chain 3 C,Map1amap1b Lc3 C,Microtubule-Associated Pr Light Chain 3 Gamma; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Map1lc3c Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
Molecule: Pleckstrin Homology Domain-Containing Family M Me Chain: B, D, F, H, J, L, N, P Fragment: Unp Residues 629-642 Synonym: Ph Domain-Containing Family M Member 1,162 Kda Ada Protein,Ap162; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Plekhm1, Kiaa0356 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet30
symmetry	Space Group: P 1	R_factor 0.200 R_Free 0.246
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.140 73.225 89.048 89.96 89.99 77.31
method	X-Ray Diffraction	resolution	2.19 Å
Gene Ontology	Chain Function Process Component A, O, M, C, K, I, G, E
Primary reference	Structural and functional analysis of the GABARAP interaction motif (GIM)., Rogov VV, Stolz A, Ravichandran AC, Rios-Szwed DO, Suzuki H, Kniss A, Lohr F, Wakatsuki S, Dotsch V, Dikic I, Dobson RC, McEwan DG, EMBO Rep. 2017 Aug;18(8):1382-1396. doi: 10.15252/embr.201643587. Epub 2017 Jun, 27. PMID:28655748

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (511 Kb) [Save to disk] Biological Unit Coordinates (5dpw.pdb1.gz) 64 Kb Biological Unit Coordinates (5dpw.pdb2.gz) 64 Kb Biological Unit Coordinates (5dpw.pdb3.gz) 64 Kb Biological Unit Coordinates (5dpw.pdb4.gz) 63 Kb Biological Unit Coordinates (5dpw.pdb5.gz) 65 Kb Biological Unit Coordinates (5dpw.pdb6.gz) 64 Kb Biological Unit Coordinates (5dpw.pdb7.gz) 64 Kb Biological Unit Coordinates (5dpw.pdb8.gz) 64 Kb CSU: Contacts of Structural Units for 5DPW Structure Factors (702 Kb) Retrieve 5DPW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5DPW from S2C, [Save to disk] Re-refined 5dpw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5DPW in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5DPW

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5dpw_H] [5dpw_M] [5dpw_E] [5dpw] [5dpw_O] [5dpw_D] [5dpw_J] [5dpw_F] [5dpw_C] [5dpw_N] [5dpw_L] [5dpw_K] [5dpw_A] [5dpw_P] [5dpw_G] [5dpw_B] [5dpw_I] SWISS-PROT database: Domain organization of by SWISSPFAM

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